Modified DNA-polymerase from carboxydothermus hydrogenoformans and its use for coupled reverse transcription and polymerase chain reaction

ABSTRACT

A purified DNA polymerase exhibiting reverse transcriptase activity in the presence of magnesium ions and/or manganese ions having reduced or no 5′-3′-exonuclease activity and substantially no RNaseH activity and obtainable from  Carboxydothermus hydrogenoformans.

[0001] This application claims priority to European patent applicationNo. 97.121151.1, filed Dec. 2, 1997.

BACKGROUND OF THE INVENTION

[0002] 1. Field of the Invention

[0003] The present invention relates to a modified DNA-polymerase havingreverse transcriptase activity and reduced 5′-3′ exonuclease activityderived from a native polymerase which is obtainable fromCarboxydothermus hydrogenoformans. Furthermore the invention relates tothe field of molecular biology and provides methods for amplifying a DNAsegment from an RNA template using an enzyme with reverse transcriptaseactivity (RT-PCR). In another aspect, the invention provides a kit forCoupled High Temperature Reverse Transcription and Polymerase ChainReaction.

[0004] 2. Description of Related Art

[0005] Heat stable DNA polymerases (EC 2.7.7.7.DNAnucleotidyltransferase, DNA-directed) have been isolated from numerousthermophilic organisms (for example: Kaledin et al. (1980), Biokhimiya45, 644-651; Kaledin et al. (1981) Biokhimiya 46, 1576-1584; Kaledin etal. (1982) Biokhimiya 47, 1785-1791; Ruttimann et al. (1985) Eur. J.Biochem. 149, 41-46; Neuner et al. (1990) Arch. Microbiol. 153,205-207). For some organisms, the polymerase gene has been cloned andexpressed (Lawyer et al. (1989) J. Biol. Chem. 264, 6427-6437; Engelkeet al. (1990) Anal. Biochem. 191, 396-400; Lundberg et al. (1991) Gene108, 1-6; Perler et al. (1992) Proc. Natl. Acad. Sci. USA 89,5577-5581).

[0006] Thermophilic DNA polymerases are increasingly becoming importanttools for use in molecular biology and there is growing interest infinding new polymerases which have more suitable properties andactivities for use in diagnostic detection of RNA and DNA, gene cloningand DNA sequencing. At present, the thermophilic DNA polymerases mostlyused for these purposes are from Thermus species like Taq polymerasefrom T. aquaticus (Brock et al. (1969) J. Bacteriol. 98, 289-297).

[0007] The term “reverse transcriptase” describes a class of polymerasescharacterized as RNA-dependent DNA-polymerases. All known reversetranscriptases require a primer to synthesize a DNA-transcript from anRNA template. Historically, reverse transcriptase has been usedprimarily to transcribe mRNA into cDNA which can then be cloned into avector for further manipulation.

[0008] Reverse transcription is commonly performed with viral reversetranscriptases like the enzymes isolated from Avian myeloblastosis virusor Moloney murine leukemia virus. Both enzymes mentioned are active inthe presence of magnesium ions but have the disadvantages to possessRNase H-activity, which destroys the template RNA during the reversetranscription reaction and have a temperature optimum at 42° C. or 37°C., respectively. Avian myoblastosis virus (AMV) reverse transcriptasewas the first widely used RNA-dependent DNA-polymerase (Verma (1977)Biochem. Biophys. Acta 473, 1). The enzyme has 5′-3′ RNA-directed DNApolymerase activity, 5′-3′ DNA directed DNA polymerase activity, andRNaseH activity. RNaseH is a processive 5′-3′ ribonuclease specific forthe RNA strand of RNA-DNA hybrids (Perbal (1984), A Practical Guide toMolecular Cloning, Wiley & Sons New York). Errors in transcriptioncannot be corrected because known viral reverse transcriptases lack the3′-5′ exonuclease activity necessary for proofreading (Saunders andSaunders (1987) Microbial Genetics Applied to Biotechnology, Croom Helm,London). A detailed study of the activity of AMV reverse transcriptaseand its associated RNaseH activity has been presented by Berger et al.,(1983) Biochemistry 22, 2365-2372.

[0009] DNA polymerases isolated from mesophilic microorganisms such asE. coli have been extensively characterized (see, for example, Bessmannet al. (1957) J. Biol. Chem. 233, 171-177 and Buttin and Kornberg (1966)J. Biol. Chem. 241, 5419-5427). E. coli DNA polymerase I (Pol I) isuseful for a number of applications including: nick-translationreactions, DNA sequencing, in vitro mutagenesis, second strand cDNAsynthesis, polymerase chain reactions (PCR), and blunt end formation forlinker ligation (Maniatis et al., (1982) Molecular Cloning: A LaboratoryManual Cold Spring Harbor, N.Y.).

[0010] Several laboratories have shown that some polymerases are capableof in vitro reverse transcription of RNA (Karkas (1973) Proc. Nat. Acad.Sci. USA 70, 3834-3838; Gulati et al. (1974) Proc. Nat. Acad. Sci USA71, 1035-1039; and Wittig and Wittig, (1978) Nuc. Acids Res. 5,1165-1178). Gulati et al. found that E. coli Pol I could be used totranscribe Qβ viral RNA using oligo(dT)₁₀ as a primer. Wittig and Wittighave shown that E.coli Pol I can be used to reverse transcribe tRNA thathas been enzymatically elongated with oligo(dA). However, as Gulati etal. demonstrated, the amount of enzyme required and the small size ofcDNA product suggest that the reverse transcriptase activity of E. coliPol I has little practical value.

[0011] Alternative methods are described using the reverse transcriptaseactivity of DNA polymerases of thermophilic organisms which are activeat higher temperatures. Reverse transcription at higher temperatures isof advantage to overcome secondary structures of the RNA template whichcould result in premature termination of products. Thermostable DNApolymerases with reverse transcriptase activities are commonly isolatedfrom Thermus species. These DNA polymerases however, show reversetranscriptase activity only in the presence of manganese ions. Thesereaction conditions are suboptimal, because in the presence of manganeseions the polymerase copies the template RNA with low fidelity.

[0012] Another feature of the commonly used reverse transcriptases isthat they do not contain 3′-5 ′ exonuclease activity. Therefore,misincorporated nucleotides cannot be removed and thus the cDNA copiesfrom the template RNA may contain a significant degree of mutations.

[0013] One of the known DNA polymerases having high reversetranscriptase activity is obtainable from Thermus thermophilus (Tthpolymerase) (WO 91/09944). Tth polymerase, as well as Taq polymerase,lacks 3′ to 5′ exonucleolytic proofreading activity. This 3′ to 5′exonuclease activity is generally considered to be desirable because itallows removal of misincorporated or unmatched bases in the newlysynthesized nucleic acid sequences. Another thermophilic pol I-type DNApolymerase isolated from Thermotoga maritima (Tma pol) has 3′ to 5′exonuclease activity. U.S. Pat. No. 5,624,833 provides means forisolating and producing Tma polymerase. However, both DNA polymerases,Tth as well as Tma polymerase, show reverse transcriptase activity onlyin the presence of manganese ions.

[0014] The DNA polymerase of Carboxydothermus hydrogenoformans showsreverse transcription activity in the presence of magnesium ions and inthe substantial absence of manganese ions and can be used to reversetranscribe RNA, to detect and amplify (in combination with athermostable DNA polymerase like Taq) specific sequences of RNA. UsingDNA polymerase of Carboxydothermus hydrogenoformans polymerase a highspecificity of transcription is observed with short incubation times. Ahigh specificity is observed using e.g. 5 min of incubation time and 33units of DNA polymerase protein. With longer incubation times also withlower amounts of Carboxydothermus hydrogenoformans polymerase specificproducts can be obtained. However an unspecific smear of products isoccurring. These unspecific products might be caused by the 5′-3′exonuclease activity of the polymerase which enables the enzyme tocleave the template at secondary structures (“RNaseH”-activity) and tocreate additional primers which can be elongated by the DNA polymeraseactivity. The thermostable DNA polymerase from Carboxydothermushydrogenoformans has been identified and cloned and is described in thecopending European application with the Application No. 96115873.0,filed Oct. 3, 1996, and incorporated herein by reference.

[0015] In summary, reverse transcriptases as MoMULV-RT or AMV-RT performreverse transcription in the presence of magnesium-ions. However, theseenzymes act at temperatures between 37° C. and 55° C. Reversetranscription at higher temperatures would be desirable becausesecondary structures can be overcome in the template in order to avoidpremature termination of the reaction and to assure the production ofcDNA without deletions. Other enzymes e.g. DNA polymerase obtainablefrom Thermus spec. act as reverse transcriptase at temperatures up to70° C. in the presence of manganese ions. These reaction conditions aresuboptimal, because in the presence of manganese ions the polymerasecopies the template RNA with low fidelity and the RNA strand will bedegraded. Degradation of the RNA strand occurs faster in the presence ofmanganese ions as in the presence of magnesium ions. Therefore, ifmanganese ions are present complexation of the manganese ions (e.g. withEDTA) is required after cDNA synthesis in order to obtain a higherfidelity during cDNA amplification in the subsequent PCR reaction.

[0016] Therefore, it is desirable to develop a reverse transcriptase

[0017] which acts at higher temperatures to overcome secondarystructures in the template to avoid premature termination of thereaction and to assure the production of cDNA without deletions

[0018] which is active in the presence of magnesium ions in order toprepare cDNA from RNA templates with higher fidelity and

[0019] which has 3′-5′-exonuclease in order to remove misincorporatednucleotides before continuation of DNA synthesis and to produce productswith low mutation frequency

[0020] which has a high specificity and produces exclusively orpredominantly RT-PCR products derived from specific primer binding.

SUMMARY OF THE INVENTION

[0021] The present invention addresses these needs and provides a DNApolymerase mutant active at higher temperatures which has reversetranscriptase activity in the presence of magnesium ions and which has3′-5′ exonuclease activity and reduced or no 5′-3′ exonuclease activity.

[0022] It is an object of this invention to provide a polymerase enzyme(EC 2.7.7.7.), characterized in that it has reverse transcriptaseactivity in the presence of magnesium ions as well as in the presence ofmanganese ions. In a further aspect the invention comprises a DNApolymerase having 3′-5′-exonuclease activity and reduced 5′-3′exonuclease activity. The enzyme according to the invention can beobtained from a polymerase obtainable from Carboxydothermushydrogenoformans (Deutsche Sammlung von Mikroorganismen und ZellkulturenGmbH, Mascheroder Weg 1b, D-38124 Braunschweig, DSM No. 8979). In afurther aspect the invention is directed to a DNA polymerase withreduced 5′-3′ exonuclease activity having reverse transcriptase activityin the presence of magnesiums ions and in the substantial absence ofmanganese ions. In a further aspect the invention comprises a DNApolymerase having a molecular mass of about 64 to 71 kDa as determinedby SDS PAGE analysis. The mutant polymerase enzyme with reduced 5′-3′exonuclease activity derived from a polymerase obtainable fromCarboxidothermus hydrogenoformans is called hereinafter Δ ChyPolymerase.

[0023] In a further aspect the invention comprises a recombinant DNAsequence that encodes DNA polymerase activity of the Δ Chy Polymerase.In a related aspect, the DNA sequence is depicted as SEQ ID No. 10 (FIG.1). In a second related aspect the invention comprises a recombinant DNAsequence that encodes essentially amino acid residues 1 to 607 (SEQ IDNo. 11, FIG. 1). In a further aspect the invention comprises arecombinant DNA plasmid that comprises the DNA sequence of the inventioninserted into plasmid vectors and which can be used to drive theexpression of the Δ Chy DNA polymerase in a host cell transformed withthe plasmid. In a further aspect the invention includes a recombinantstrain comprising the vector pDS56 carrying the Δ Chy DNA polymerasegene and designated pΔ₂₋₂₂₅AR₄. The E.coli strain XL1 carrying theplasmid pΔ₂₋₂₂₅AR₄ was deposited on the Deutsche Sammlung vonMikroorganismen und Zellkulturen GmbH, Mascherorder Weg 1b, D-38124Braunschweig DSM No. 11854 (BMTU 7307) is designated E.coli GA1.

BRIEF DESCRIPTION OF THE DRAWINGS

[0024]FIG. 1 shows the nucleic acid and amino acid sequence of the“Klenow fragment” of Chy polymerase designated Δ Chy.

[0025]FIG. 2 shows the reverse transcriptase activity of Δ Chy independence of magnesium and manganese salt.

[0026]FIG. 3 shows the reverse transcription and amplification of a 997bp fragment of the β-Actin gene from total mouse liver RNA using Δ Chyand the Expand HiFi-System and decreasing amounts of RNA.

[0027]FIG. 4 shows the reverse transcription and amplification of a 997bp fragment of β-actin from total mouse liver RNA in comparison to Tthpolymerase. Reverse transcription was either coupled with amplification(“one tube”) using the Expand HiFi-System from Boehringer Mannheim, orafter reverse transcription the Expand HiFi-System from BoehringerMannheim was added to the reaction mixture for the subsequentamplification reaction (“two tube”).

[0028]FIG. 5 shows the reverse transcription and amplification of a 1.83kb fragment of Dystrophin from total human muscle RNA.

[0029]FIG. 6 shows the reverse transcription and amplification of a 324bp fragment of β-actin from total mouse liver RNA with various amountsof Chy polymerase and various incubation times. FIG. 7 showsschematically the construction of the clone encoding Δ Chy from theclone encoding the wild type gene.

DETAILED DESCRIPTION OF THE INVENTION

[0030] In referring to a peptide chain as being comprised of a series ofamino acids “substantially or effectively” in accordance with a listoffering no alternatives within itself, we include within that referenceany versions of the peptide chain bearing substitutions made to one ormore amino acids in such a way that the overall structure and theoverall function of the protein composed of that peptide chain issubstantially the same as—or undetectably different to—that of theunsubstituted version. For example it is generally possible to exchangealanine and valine without greatly changing the properties of theprotein, especially if the changed site or sites are at positions notcritical to the morphology of the folded protein.

[0031] 3′-5′ exonuclease activity is commonly referred as “proofreading”or “editing” activity of DNA polymerases. It is located in the smalldomain of the large fragment of Type A polymerases. This activityremoves mispaired nucleotides from the 3′ end of the primer terminus ofDNA in the absence of nucleoside triphosphates (Kornberg A. and Baker T.A. (1992) DNA Replication W. H. Freemann & Company, New York). Thisnuclease action is suppressed by deoxynucleoside triphosphates if theymatch to the template and can be incorporated into the polymer. The3′-5′ exonuclease activity of the claimed DNA polymerase can be measuredas degradation or shortening of a 5′-digoxygenin-labeled oligonucleotideannealed to template DNA in the absence or presence ofdeoxyribonucleoside triphosphates or on DNA fragments in the absence orpresence of deoxyribonucleoside triphosphates.

[0032]Carboxydothermus hydrogenoformans DNA polymerase is the first DNApolymerase isolated from thermophilic eubacteria with a higher activityin the presence of magnesium ions than in the presence of manganese ionsas shown in FIG. 2. The reverse transcriptase activity in dependence ofmagnesium is of advantage since the DNA polymerases synthesize DNA withhigher fidelity in the presence of magnesium than in the presence ofmanganese (Beckmann R. A. et al. (1985) Biochemistry 24, 5810-5817;Ricchetti M. and Buc H. (1993) EMBO J. 12, 387-396). Low fidelity DNAsynthesis is likely to lead to mutated copies of the original template.In addition, Mn²⁺ ions have been implicated in an increased rate of RNAdegradation, particularly at higher temperatures and this can cause thesynthesis of shortened products in the reverse transcription reaction.

[0033] The DNA sequence (SEQ ID No.: 10) of Δ Chy polymerase and thederived amino acid sequence (SEQ ID No.: 11) of the enzyme are shown inFIG. 1. The molecular weight deduced from the sequence is 70.3 kDa, inSDS polyacrylamide gel electrophoresis however Δ Chy polymerase has anelectrophoretic mobility of approximately 65 kDa.

[0034] The Δ Chy DNA Polymerase has reduced 5′-3′-exonuclease activityand has a temperature optimum at 72° C. and exhibits reversetranscriptase activity at temperatures between 50° C. and 75° C.

[0035] When using Δ Chy DNA Polymerase obtainable from Carboxydothermushydrogenoformans having reduced 5′-3′-exonuclease activity in RT-PCR asreverse transcriptase with subsequent PCR reaction using Taq-polymeraseas PCR enzyme a remarkable high sensitivity is achieved (FIG. 3). Thesensitivity of Δ Chy DNA Polymerase in RT-PCR is higher than thesensitivity of e.g. DNA polymerase from Thermus thermophilus (Tthpolymerase) (Example 3, FIG. 4). Δ Chy DNA Polymerase also exhibits highsensitivity by amplifying a 1.83 kB fragment from total RNA from humanmuscle (FIG. 5). The error rate of Δ Chy DNA Polymerase is 1.58×10⁻⁴mutations per nucleotide per cycle and is therewith lower than the errorrate of Tth Polymerase which is 2.37×10⁻⁴ mutations per nucleotide percycle. This results in higher fidelity of Δ Chy DNA polymerase incomparison to Tth Polymerase.

[0036]Carboxydothermus hydrogenoformans was isolated from a hot springin Kamchatka by V. Svetlichny. A sample of C. hydrogenoformans wasdeposited on the Deutsche Sammlung von Mikroorganismen und ZellkulturenGmbH (DSM) under the terms of the Budapest Treaty and received AccessionNumber DSM 8979. The thermostable polymerase isolated fromCarboxydothermus hydrogenoformans has a molecular weight of 100 to 105KDa. The thermostable enzyme possesses 5′-3′ polymerase activity, a3′-5′-exonuclease activity and a reverse transcriptase-activity which isMg⁺⁺-dependent. The thermostable enzyme may be native or recombinant andmay be used for first- and second-strand cDNA synthesis, in cDNAcloning, DNA sequencing, DNA labeling and DNA amplification.

[0037] For recovering the native protein C.hydrogenoformans may be grownusing any suitable technique, such as the technique described bySvetlichny et al. (1991) System. Appl. Microbiol. 14, 205-208. Aftercell growth one preferred method for isolation and purification of theenzyme is accomplished using the multi-step process as follows:

[0038] The cells are thawed, suspended in buffer A (40 mM Tris-HCl, pH7.5, 0.1 mM EDTA, 7 mM 2-mercaptoethanol, 0.4 M NaCl, 10 mM Pefabloc)and lysed by twofold passage through a Gaulin homogenizer. The rawextract is cleared by centrifugation, the supernatant dialyzed againstbuffer B (40 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 7 mM 2-mercaptoethanol,10% Glycerol) and brought onto a column filled with Heparin-Sepharose(Pharmacia). In each case the columns are equilibrated with the startingsolvent and after the application of the sample washed with thethreefold of its volume with this solvent. Elution of the first columnis performed with a linear gradient of 0 to 0.5 M NaCl in Buffer B. Thefractions showing polymerase activity are pooled and ammonium sulfate isadded to a final concentration of 20%. This solution is applied to ahydrophobic column containing Butyl-TSK-Toyopearl (TosoHaas). The columnis eluted with a falling gradient of 20 to 0% ammonium sulfate. The poolcontaining the activity is dialysed and again transferred to a column ofDEAE-Sepharose (Pharmacia) and eluted with a linear gradient of 0-0.5 MNaCl in buffer B. The fourth column contains Tris-Acryl-Blue (Biosepra)and is eluted as in the preceding case. Finally the active fractions aredialyzed against buffer C (20 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 7.0 mM2-mercaptoethanol, 100 mM NaCl, 50% Glycerol.

[0039] DNA polymerase activity was measured by incorporation ofdigoxigenin-labeled dUTP into the synthesized DNA and detection andquantification of the incorporated digoxigenin essentially according tothe method described in Höltke, H. -J.; Sagner, G; Kessler, C. andSchmitz, G. (1992) Biotechniques 12, 104-113. The reaction is performedin a reaction volume of 50 μl containing 1 or 2 μl of diluted (0.05U-0.01 U) DNA polymerase and 50 mM Tris-HCl, pH 8.5; 12.5 mM (NH₄)₂SO₄;10 mM KCl; 5 mM MgCl₂; 10 mM 2-mercaptoethanol; 33 μM dNTPs; 200 μg/mlBSA; 12 μg of DNAse I-activated DNA from calf thymus and 0.036 μMdigoxigenin-dUTP.

[0040] The samples are incubated for 30 min. at 72° C., the reaction isstopped by addition of 2 μl 0.5 M EDTA, and the tubes placed on ice.After addition of 8 μl 5 M NaCl and 150 μl of Ethanol (precooled to −20°C.) the DNA is precipitated by incubation for 15 min. on ice andpelleted by centrifugation for 10 min at 13000×rpm and 4° C. The pelletis washed with 100 μl of 70% Ethanol (precooled to −20° C.) and 0.2 MNaCl, centrifuged again and dried under vacuum.

[0041] The pellets are dissolved in 50 μl Tris-EDTA (10 mM/0.1 mM; pH7.5). 5 μl of the sample are spotted into a well of a nylon membranebottomed white microwave plate (Pall Filtrationstechnik GmbH, Dreieich,FRG, product no: SM045BWP). The DNA is fixed to the membrane by bakingfor 10 min. at 70° C. The DNA loaded wells are filled with 100 μl of0.45 μm-filtrated 1% blocking solution (100 mM maleic acid, 150 mM NaCl,1% (w/v) casein, pH 7.5). All following incubation steps are done atroom temperature. After incubation for 2 min. the solution is suckedthrough the membrane with a suitable vacuum manifold at −0.4 bar. Afterrepeating the washing step, the wells are filled with 100 μl of a1:10,000-dilution of Anti-digoxigenin-AP, Fab fragments (BoehringerMannheim, FRG, no: 1093274) diluted in the above blocking solution.After incubation for 2 min. and sucking this step is repeated once. Thewells are washed twice under vacuum with 200 μl each time washing-buffer1 (100 mM maleic-acid, 150 mM NaCl, 0.3%(v/v) Tween™ 20, pH 7.5). Afterwashing another two times under vacuum with 200 μl each timewashing-buffer 2 (10 mM Tris-HCl, 100 mM NaCl, 50 mM MgCl₂, pH 9.5) thewells are incubated for 5 min. with 50 μl of CSPD™ (Boehringer Mannheim,no: 1655884), diluted 1:100 in washing-buffer 2, which serves as achemiluminescent substrate for the alkaline phosphatase. The solution issucked through the membrane and after 10 min. incubation the RLU/s(Relative Light Unit per second) are detected in a Luminometer e.g.MicroLumat LB 96 P (EG&G Berthold, Wilbad, FRG).

[0042] With a serial dilution of Taq DNA polymerase a reference curve isprepared from which the linear range serves as a standard for theactivity determination of the DNA polymerase to be analyzed.

[0043] The Determination of reverse transcriptase activity is performedessentially as described for determination of DNA polymerase activityexcept that the reaction mixture consists of the following components: 1μg of polydA-(dT)₁₅, 33 μM of dTTP, 0.36 μM of digoxigenin-dUTP, 200mg/ml BSA, 10 mM Tris-HCl, pH 8.5, 20 mM KCl, 5 mM MgCl₂, 10 mM DTE andvarious amounts of DNA polymerase. The incubation temperature used is50° C.

[0044] Isolation of recombinant DNA polymerase from Carboxydothermushydrogenoformans may be performed with the same protocol or with othercommonly used procedures.

[0045] The production of a recombinant form of Carboxydothermushydrogenoformans DNA polymerase generally includes the following steps:chromosomal DNA from Carboxydothermus hydrogenoformans is isolated bytreating the cells with detergent e.g. SDS and a proteinase e.g.Proteinase K. The solution is extracted with phenol and chloroform andthe DNA purified by precipitation with ethanol. The DNA is dissolved inTris/EDTA buffer and the gene encoding the DNA polymerase isspecifically amplified by the PCR technique using two mixedoligonucleotides (primer 1 and 2). These oligonucleotides, described bySEQ ID No.: 1 and SEQ ID No.: 2, were designed on the basis of conservedregions of family A DNA polymerases as published by Braithwaite D. K.and Ito J. (1993) Nucl. Acids Res. 21, 787-802. The specificallyamplified fragment is ligated into an vector, preferably the pCR™IIvector (Invitrogen) and the sequence is determined by cycle-sequencing.Complete isolation of the coding region and the flanking sequences ofthe DNA polymerase gene can be performed by restriction fragmentation ofthe Carboxydothermus hydrogenoformans DNA with another restrictionenzyme as in the first round of screening and by inverse PCR (Innis etal., (1990) PCR Protocols; Academic Press, Inc., 219-227). This can beaccomplished with synthesized oligonucleotide primers binding at theouter DNA sequences of the gene part but in opposite orientation. Theseoligonucleotides described by SEQ ID Nos. 3 and 4, were designed on thebasis of the sequences which were determined by sequencing of the firstPCR product described above. As template DNA from Carboxydothermushydrogenoformans is used which is cleaved by restriction digestion andcircularized by contacting with T4 DNA ligase. To isolate the codingregion of the entire polymerase gene, another PCR is performed usingprimers as shown in SEQ ID Nos. 5 and 6. The complete DNA polymerasegene is amplified directly from genomic DNA with primers suitable forintroducing ends compatible with the linearized expression vector. SEQID No.1: Primer 1: 5′-CCN AAY YTN CAR AAY ATH-3′ SEQ ID No.2: Primer 2:5′-YTC RTC RTG NAC YTG-3′ SEQ ID No.3: Primer 3: 5′-GGG CGA AGA CGC TATATT CCT GAG C-3′ SEQ ID NO.4: Primer 4: 5′-GAA GCC TTA ATT CAA TCT GGGAAT AAT C-3′ SEQ ID NO.5: Primer 5: 5′-CGA ATT CAA TCC ATG GGA AAA GTAGTC CTG GTG GAT-3′ SEQ ID NO.6: Primer 6: 5′-CGA ATT CAA GGA TCC TTA CTTCGC TTC ATA CCA GTT-3′

[0046] The gene is operably linked to appropriate control sequences forexpression in either prokaryotic or eucaryotic host/vector systems. Thevector preferably encodes all functions required for transformation andmaintenance in a suitable host, and may encode selectable markers and/orcontrol sequences for polymerase expression. Active recombinantthermostable polymerase can be produced by transformed host cultureseither continuously or after induction of expression. Activethermostable polymerase can be recovered either from host cells or fromthe culture media if the protein is secreted through the cell membrane.

[0047] The use of a plasmid as an appropriate vector has shown to beadvantageous, particularly pDS56 (Stüber, D., Matile, H. and Garotta, G.(1990) Immunological Methods, Letkovcs, I. and Pernis, B., eds). Theplasmid carrying the Carboxydothermus hydrogenoformans DNA polymerasegene is then designated pAR4.

[0048] According to the present invention the use of the E. coli strainBL21 (DE3) pUBS520 (Brinkmann et al., (1989) Gene 85, 109-114) has shownto be advantageous. The E.coli strain BL 21 (DEB) pUBS 520 transformedwith the plasmid pAR4 is then designated AR96 (DSM No 11179).

[0049] The mutant ΔChy was obtained by deletion of an N-terminalfragment of the recombinant wild type Carboxydothermus hydrogenoformansDNA polymerase using inverse PCR (Innis et al., (1990) PCR Protocols;Academic Press, Inc., p 219-227). The reverse primer used iscomplementary to the cloning site of the expression vector pDS56(Stüber, D., Matile, H. and Garotta, G. (1990) Immunological Methods,Letkovcs, I. and Pernis, B., eds.) at the Nco I restriction site (bases120-151) and has the sequence:

[0050] SEQ ID No. 7:

[0051] Primer 7: 5′-CGG TAA ACC CAT GGT TAA TTT CTC CTC TTT AAT GAATTC-3′.

[0052] This primer contains additional 7 bases at the 5′ end to ensure abetter binding of the Nco I restriction enzyme in the subsequentrestriction enzyme cleavage. The second (forward) primer wascomplementary to bases 676-702 of the wild type gene and has thesequence:

[0053] SEQ ID No. 8:

[0054] Primer 8: 5′-CGG GAA TCC ATG GAA AAG CTT GCC GAA CAC GAA AATTTA-3′

[0055] The forward primer also contained an additional Nco I restrictionsite and additional 7 bases at the 5′-end. Plasmid pDS56 DNA containingthe polymerase-gene of Carboxydothermus hydrogenoformans at the NcoI/BamHI restriction sites was used as template for PCR. The PCR reactionwas performed on the circular plasmid DNA pAR4. The fragment encodingthe mutated Carboxydothermus hydrogenoformans DNA polymerase (Δ Chy) andthe vector DNA were amplified as linear DNA by PCR using the Expand HighFidelity PCR System (Boehringer Mannheim) according to the supplier'sspecifications (FIG. 7). The length of the gene encoding Δ Chy is 1821bp.

[0056] Amplification (Perkin Elmer GeneAmp 9600 thermocycler) wascarried out with the following conditions: 2 min 94° C., (10 sec 94° C.;30 sec 65° C.; 4 min 68° C.)×10; (10 sec 94° C.; 30 sec 65° C.; 4 min68° C.)+ cycle elongation of 20 sec for each cycle)×20; 7 min 72° C.;After PCR the amplified DNA was purified using the High Pure PCR ProductPurification Kit (Boehringer Mannheim) and digested with NcoI (3U/μgDNA) for 16 h (Boehringer Mannheim) according to the supplier'sspecifications.

[0057] For extraction with Phenol/Chloroform/Isoamylalcohol (24:24:1)the volume of the sample was raised to 100 μl with TE. After extractionthe DNA was precipitated by adding {fraction (1/10)} volumes of 3MSodium Acetate, pH 5.2 and 2 volumes of EtOH. The DNA was circularizedusing the Rapid DNA Ligation Kit (Boehringer Mannheim) according to thesupplier's specification. The ligated products were introduced into E.coli XL1-Blue by transformation according to the procedure of Chung, C.T. et al. (1989) Proc. Natl. Acad. Sci. USA 86, 2172-2175. Transformantswere plated on L-agar containing 100 μg/ml ampicillin to allow selectionof recombinants. Colonies were picked and grown in L-broth containing100 μg/ml ampicillin. Plasmid DNA was prepared with the High PurePlasmid Isolation Kit (Boehringer Mannheim) according to the supplier'sspecification. The plasmids were screened for insertions by digestionwith NcoI/BamHI. Strains containing the genes of interest were grown inL-broth supplemented with 100 μg/ml ampicillin and tested for theexpression of DNA polymerase/reverse transcriptase activity by inductionof exponentially growing culture with 1 mM IPTG and assaying theheat-treated extracts (72° C.) for DNA polymerase/reverse transcriptaseactivity as described above (determination of DNA polymerase activityand determination of reverse transcriptase activity).

[0058] The present invention provides improved methods for efficientlytranscribing RNA and amplifying RNA or DNA. These improvements areachieved by the discovery and application of previously unknownproperties of thermoactive DNA polymerases with reverse transcriptaseactivity.

[0059] The enzyme of this invention may be used for any purpose in whichsuch enzyme activity is necessary or desired. In a particularlypreferred embodiment, the enzyme catalyzes reverse transcription of RNAwhich is amplified as DNA by a second DNA polymerase present in theamplification reaction known as RT-PCR (Powell et al. (1987) Cell 50,831-840). Any ribonucleic acid sequence, in purified or nonpurifiedform, can be utilized as the starting nucleic acid(s), provided itcontains or is suspected to contain the specific nucleic acid sequencedesired. The nucleic acid to be amplified can be obtained from anysource, for example, from plasmids such as pBR322, from cloned RNA, fromnatural RNA from any source, including bacteria, yeast, viruses,organelles, and higher organisms such as plants and animals, or frompreparations of nucleic acids made in vitro.

[0060] RNA may be extracted from blood, tissue material such aschorionic villi, or amniotic cells by a variety of techniques. See,e.g., Maniatis et al., (1982) Molecular Cloning: A Laboratory Manual(Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.) pp. 280-281.Thus the process may employ, for example, RNA, including messenger RNA,which RNA may be single-stranded or double-stranded. In addition, aDNA-RNA hybrid which contains one strand of each may be utilized.

[0061] The amplification of target sequences from RNA may be performedto proof the presence of a particular sequence in the sample of nucleicacid to be analyzed or to clone a specific gene. Δ Chy DNA polymerase isvery useful for these processes. Due to its 3′-5′ exonuclease activityit is able to synthesize products with higher accuracy as the reversetranscriptases of the state of the art.

[0062] Δ Chy DNA polymerase may also be used to simplify and improvemethods for detection of RNA target molecules in a sample. In thesemethods Δ Chy DNA polymerase from Carboxydothermus hydrogenoformans maycatalyze: (a) reverse transcription and (b) second strand cDNAsynthesis. The use of DNA polymerase from Carboxydothermushydrogenoformans may be used to perform RNA reverse transcription andamplification of the resulting complementary DNA with enhancedspecificity and with fewer steps than previous RNA cloning anddiagnostic methods.

[0063] Another aspect of the invention comprises a kit for performingRT-PCR comprising Δ Chy polymerase, reaction buffers, nucleotidemixtures, and optionally a thermostable DNA polymerase for detection andamplification of RNA either in a one step reaction or for reversetranscription of the template RNA and subsequent amplification of thecDNA product.

[0064] The following examples describe the invention in greater detail:

EXAMPLE 1

[0065] Reverse Transcription of a 324 bp β-Actin Fragment with Chy WildType DNA Polymerase Used as Reverse Transcriptase Followed by PCR withTaq-Polymerase (FIG. 6).

[0066] The reaction mixture (20 μl) contained 200 ng total mouse liverRNA, 200 μM dNTP, 10 mM Tris-HCl, pH 8.8, 5 mM DTT, 10 mM2-mercaptoethanol, 15 mM KCl, 4.5 mM MgCl₂, 0.02 mg/ml BSA, 20 pmol ofreverse primer (β-actin reverse: 5′-AAT TCG GAT GGC TAC GTA CAT GGCTG-3′ [SEQ ID NO: 9]) and Chy-polymerase 33 units (lanes 1, 4, 7, 10,13, 16), 13.2 units (lanes 2, 5, 8, 11, 14, 17) and 6.6 units (lanes 3,6, 9, 12, 15, 18). Reactions were incubated for 5 min (lanes 1 to 6), 10min (lanes 7 to 12) and 15 min (lanes 13 to 18) at 70° C. 20 μl of thereverse transcription reaction was used as template for PCR (100 μlreaction volume) with Taq-polymerase (Boehringer Mannheim) according tothe supplier's specification using 20 pmol of forward and reverse primer(Primer sequence “β-actin forward”: 5′AGC TTG CTG TAT TCC CCT CCA TCGTG-3′ [SEQ ID NO: 12], primer sequence “β-actin reverse”: 5′-AAT TCG GATGGC TAC GTA CAT GGC TG-3′ [SEQ ID NO: 9]) and 200 μM dNTP's.Amplification was carried out using the following temperature profile: 2min 94° C.; (10 sec 94° C.; 30 sec 60° C.; 30 sec 72° C.)×30; 7 min 72°C.

EXAMPLE 2

[0067] Construction of the Vector Expressing Δ Chy.

[0068] The mutant was obtained by deletion of an N-terminal fragment ofrecombinant wild type Carboxydothermus hydrogenoformans DNA polymeraseusing inverse PCR (Innis et al., (1990) PCR Protocols; Academic Press,Inc., p 219-227). The reverse primer used is complementary to thecloning site of the expression vector pDS56 (Stüber, D., Matile, H. andGarotta, G. (1990) Immunological Methods, Letkovcs, I. and Pernis, B.,eds.) at the Nco I restriction site (bases 120-151) and has thesequence: 5′-CGG TAA ACC CAT GGT TAA TTT CTC CTC TTT AAT GAA TTC-3′ (SEQID NO: 7). This primer contains additional 7 bases at the 5′ end toensure a better binding of the Nco I restriction enzyme in thesubsequent restriction enzyme cleavage. The second (forward) primer, wascomplementary to bases 676-702 of the wild type gene (sequence: 5′-CGGGAA TCC ATG GAA AAG CTT GCC GAA CAC GAA AAT TTA-3′ [SEQ ID NO: 8]). Theforward primer also contained an additional Nco I restriction site andadditional 7 bases at the 5′-end. Plasmid pDS56 DNA containing thepolymerase-gene of Carboxydothermus hydrogenoformans at the Nco I/BamHIrestriction sites was used as template for PCR. The PCR reaction wasperformed on circular plasmid DNA pAR4. The fragment of Carboxydothermushydrogenoformans DNA polymerase (ΔChy) and the vector DNA were amplifiedas linear DNA by PCR using the Expand High Fidelity PCR System(Boehringer Mannheim) according to the supplier's specifications. Thelength of the gene encoding Δ Chy is 1821 bp. Amplification (PerkinElmer GeneAmp 9600 thermocycler) was carried out with the followingconditions: 2 min 94° C., (10 sec 94° C.; 30 sec 65° C.; 4 min 68°C.)×10; (10 sec 94° C.; 30 sec 65° C.; 4 min 68° C.)+cycle elongation of20 sec for each cycle)×20; 7 min 72° C.

[0069] After PCR the amplified DNA was purified using the High Pure PCRProduct Purification Kit (Boehringer Mannheim) and digested with NcoI(3U/μg DNA) for 16 h (Boehringer Mannheim) according to the supplier'sspecifications. For extraction with Phenol/Chloroform/Isoamylalcohol(24:24:1) the volume of the sample was raised to 100 μl with TE. Afterextraction the DNA was precipitated by adding {fraction (1/10)} volumesof 3M Sodium Acetate, pH 5.2 and 2 volumes of EtOH. The DNA wascircularized using the Rapid DNA Ligation Kit (Boehringer Mannheim)according to the supplier's specification. The ligated products wereintroduced into E. coli XL1-Blue by transformation according to theprocedure of Chung, C. T. et al. (1989) Proc. Natl. Acad. Sci. USA 86,2172-2175. Transformants were plated on L-agar containing 100 μg/mlampicillin to allow selection of recombinants. Colonies were picked andgrown in L-broth containing 100 μg/ml ampicillin. Plasmid DNA wasprepared with the High Pure Plasmid Isolation Kit (Boehringer Mannheim)according to the supplier's specification. The plasmids were screenedfor insertions by digestion with NcoI/BamHI. Strains containing thegenes of interest were grown in L-broth supplemented with 100 μg/mlampicillin and tested for the expression of DNA polymerase/reversetranscriptase activity by induction of exponentially growing culturewith 1 mM IPTG and assaying the heat-treated extracts (72° C.) for DNApolymerase/reverse transcriptase activity as described above(determination of DNA polymerase activity and determination of ReverseTranscriptase activity). (FIG. 7)

EXAMPLE 3

[0070] Reverse Transcription and Amplification of a 997 bp Fragment ofβ-actin from Total Mouse Liver RNA. Comparison of Δ Chy with TthPolymerase in the Reverse Transcription Reaction (FIG. 4) Either in aCoupled RT-PCR Reaction (“one tube”) or in Consecutive Steps, ReverseTranscription, Addition of Polymerase and Amplification of the cDNAProduct of the First Step.

[0071] “One Tube” System:

[0072] The reactions (50 μl) contained 10 mM Tris-HCl, pH 8.8 at 25° C.,15 mM KCl, 2.5 mM MgCl₂, 400 μM of each dNTP, decreasing amounts ofmouse total RNA (Clonetech) as indicated in the figure, 300 nM of eachprimer, 60 units of Δ Chy and 3.5 units of the Expand HiFi enzyme mix(Boehringer Mannheim GmbH). All reactions were incubated at 60° C. for30 min (RT step). Amplification followed immediately with followingcycle profile (Perkin Elmer GeneAmp 9600 thermocycler): 30 sec. at 94°C.; (30 sec at 94° C., 30 sec at 60° C., 1 min. at 68° C.)×10; (30 sec.at 94° C., 30 sec. at 60° C., 1 min. at 68° C.+cyle elongation of 5 sec.for each cycle)×20; 7 min at 68° C.;

[0073] “Two Tube” System:

[0074] Reverse transcription is performed in 10 mM Tris-HCl, pH 8.8, 15mM (NH₄)₂SO₄, 0.1% Tween, 4.5 mM MgCl₂, 2% DMSO, 800 μM dNTPs, 300nmoles of each primer, 60 units of Δ Chy, various amounts of total mousemuscle RNA as indicated in the figure. The reaction was performed in avolume of 25 μl for 30 min at 60° C. 5 μl of this reaction are used forthe amplification with the Expand HiFi-system from Boehringer Mannheim.Amplification was performed with 2.6 units of polymerase mixture in areaction volume of 25 μl. The following temperature cycling conditionswere used: 30 sec. at 94° C., (30 sec. at 94° C., 30 sec at 60° C., 1min at 68° C.)×10, (30 sec. at 94° C., 30 sec. at 60° C., 1 min at 68°C.+cycle elongation for 5 sec for each cycle)×20.

[0075] As a control reaction the same template-primer system was usedfor RT-PCR with Tth polymerase (Boehringer Mannheim). The reaction wasset up according to the supplier's specifications for the “one step”variant.

LITERATURE CITED

[0076] Beckmann R. A. et al. (1985) Biochemistry 24, 5810-5817

[0077] Berger et al., (1983) Biochemistry 22, 2365-2372

[0078] Bessmann et al. (1957) J. Biol. Chem. 233, 171-177

[0079] Braithwaite D. K. and Ito J. (1993) Nucl. Acids Res. 21, 787-802

[0080] Brinkmann U. et al. (1989) Gene 85, 109-114.

[0081] Brock et al. (1969) J. Bacteriol. 98, 289-297

[0082] Buttin and Kornberg (1966) J. Biol. Chem. 241, 5419-5427

[0083] Chung, C. T. et al. (1989) Proc. Natl. Acad. Sci. USA 86,2172-2175

[0084] Engelke et al. (1990) Anal. Biochem. 191, 396-400.

[0085] Gulati et al. (1974) Proc. Nat. Acad. Sci. USA 71, 1035-1039

[0086] Höltke, H. -J.; Sagner, G; Kessler, C. and Schmitz, G. (1992)Biotechniques 12, 104-113.

[0087] Innis et al., (1990) PCR Protocols; Academic Press, Inc., 219-227

[0088] Kaledin et al. (1980), Biokhimiya 45, 644-651.

[0089] Kaledin et al. (1981) Biokhimiya 46, 1576-1584.

[0090] Kaledin et al. (1982) Biohkimiya 47, 1785-1791.

[0091] Karkas (1973) Proc. Nat. Acad. Sci. USA 70, 3834-3838

[0092] Kornberg A. and Baker T. A. (1992) DNA Replication W. H. Freemann& Company, New York.

[0093] Lawyer et al. (1989) J. Biol. Chem. 264, 6427-6437.

[0094] Lundberg et al. (1991) Gene 108, 1-6.

[0095] Maniatis et al. (1982) Molecular Cloning: A Laboratory Manual,Cold Spring Harbor, N.Y.

[0096] Neuner et al. (1990) Arch. Microbiol. 153, 205-207.

[0097] Powell et al. (1987) Cell 50, 831-840

[0098] Perbal (1984), A Practical Guide to Molecular Cloning, Wiley &Sons New York

[0099] Perler et al. (1992) Proc. Natl. Acad. Sci USA 89, 5577-5581.

[0100] Powell et al. (1987) Cell 50, 831-840

[0101] Ricchetti M. and Buc H. (1993) EMBO J. 12, 387-396.

[0102] Ruttimann et al. (1985) Eur. J. Biochem. 149, 41-46.

[0103] Saunders and Saunders (1987) Microbial Genetics Applied toBiotechnology, Croom Helm, London

[0104] Spanos A. and Hübscher U. (1983) Methods in Enzymology 91,263-277.

[0105] Stüber D., Matile H. and Garotta G. (1990) Immunological Methods,Letkovcs, I and Pernis, B., eds.

[0106] Svetlichny et al. (1991) System. Appl. Microbiol., 14, 205-208.

[0107] Triglia T. et al. (1988) Nucleic Acids Res. 16, 8186.

[0108] Verma (1977) Biochem. Biophys. Acta 473, 1

[0109] Wittig and Wittig, (1978) Nuc. Acids Res. 5, 1165-1178

1 12 1 18 DNA Artificial Sequence Description of artificial sequenceamplification primer 1 ccnaayytnc araayath 18 2 15 DNA ArtificialSequence Description of artificial sequence amplification primer 2ytcrtcrtgn acytg 15 3 25 DNA Artificial Sequence Description ofartificial sequence amplification primer 3 gggcgaagac gctatattcc tgagc25 4 28 DNA Artificial Sequence Description of artificial sequenceamplification primer 4 gaagccttaa ttcaatctgg gaataatc 28 5 36 DNAArtificial Sequence Description of artificial sequence amplificationprimer 5 cgaattcaat ccatgggaaa agtagtcctg gtggat 36 6 36 DNA ArtificialSequence Description of artificial sequence amplification primer 6cgaattcaag gatccttact tcgcttcata ccagtt 36 7 39 DNA Artificial SequenceDescription of artificial sequence amplification primer 7 cggtaaacccatggttaatt tctcctcttt aatgaattc 39 8 39 DNA Artificial SequenceDescription of artificial sequence amplification primer 8 cgggaatccatggaaaagct tgccgaacac gaaaattta 39 9 26 DNA Artificial SequenceDescription of artificial sequence amplification primer 9 aattcggatggctacgtaca tggctg 26 10 1824 DNA Carboxydothermus hydrogenoformans CDS(1)..(1824) 10 atg gaa aag ctt gcc gaa cac gaa aat tta gca aaa ata tcgaaa caa 48 Met Glu Lys Leu Ala Glu His Glu Asn Leu Ala Lys Ile Ser LysGln 1 5 10 15 tta gct aca atc ctg cgg gaa ata ccg tta gaa atc tcc ctggaa gat 96 Leu Ala Thr Ile Leu Arg Glu Ile Pro Leu Glu Ile Ser Leu GluAsp 20 25 30 tta aaa gtt aaa gaa cct aat tat gaa gaa gtt gct aaa tta tttctt 144 Leu Lys Val Lys Glu Pro Asn Tyr Glu Glu Val Ala Lys Leu Phe Leu35 40 45 cac ctt gag ttt aaa agc ttt tta aaa gaa ata gaa cca aaa ata aag192 His Leu Glu Phe Lys Ser Phe Leu Lys Glu Ile Glu Pro Lys Ile Lys 5055 60 aaa gaa tac cag gaa ggt aaa gat ttg gtg caa gtt gaa act gta gaa240 Lys Glu Tyr Gln Glu Gly Lys Asp Leu Val Gln Val Glu Thr Val Glu 6570 75 80 acg gaa gga cag att gca gta gtt ttt agt gat gga ttt tat gtt gat288 Thr Glu Gly Gln Ile Ala Val Val Phe Ser Asp Gly Phe Tyr Val Asp 8590 95 gac ggg gaa aaa aca aag ttt tac tct tta gac cgg ctg aat gaa ata336 Asp Gly Glu Lys Thr Lys Phe Tyr Ser Leu Asp Arg Leu Asn Glu Ile 100105 110 gag gaa ata ttt agg aat aaa aaa att att acc gac gat gcc aaa gga384 Glu Glu Ile Phe Arg Asn Lys Lys Ile Ile Thr Asp Asp Ala Lys Gly 115120 125 att tat cat gtc tgt tta gaa aaa ggt ctg act ttt ccc gaa gtt tgt432 Ile Tyr His Val Cys Leu Glu Lys Gly Leu Thr Phe Pro Glu Val Cys 130135 140 ttt gat gcg cgg att gca gct tat gtt tta aac ccg gcc gac caa aat480 Phe Asp Ala Arg Ile Ala Ala Tyr Val Leu Asn Pro Ala Asp Gln Asn 145150 155 160 ccc ggc ctc aag ggg ctt tat cta aag tat gac tta ccg gtg tatgaa 528 Pro Gly Leu Lys Gly Leu Tyr Leu Lys Tyr Asp Leu Pro Val Tyr Glu165 170 175 gat gta tct tta aac att aga ggg ttg ttt tat tta aaa aaa gaaatg 576 Asp Val Ser Leu Asn Ile Arg Gly Leu Phe Tyr Leu Lys Lys Glu Met180 185 190 atg aga aaa atc ttt gag cag gag caa gaa agg tta ttt tat gaaata 624 Met Arg Lys Ile Phe Glu Gln Glu Gln Glu Arg Leu Phe Tyr Glu Ile195 200 205 gaa ctt cct tta act cca gtt ctt gct caa atg gag cat acc ggcatt 672 Glu Leu Pro Leu Thr Pro Val Leu Ala Gln Met Glu His Thr Gly Ile210 215 220 cag gtt gac cgg gaa gct tta aaa gag atg tcg tta gag ctg ggagag 720 Gln Val Asp Arg Glu Ala Leu Lys Glu Met Ser Leu Glu Leu Gly Glu225 230 235 240 caa att gaa gag tta atc cgg gaa att tat gtg ctg gcg ggggaa gag 768 Gln Ile Glu Glu Leu Ile Arg Glu Ile Tyr Val Leu Ala Gly GluGlu 245 250 255 ttt aac tta aac tcg ccc agg cag ctg gga gtt att ctt tttgaa aaa 816 Phe Asn Leu Asn Ser Pro Arg Gln Leu Gly Val Ile Leu Phe GluLys 260 265 270 ctt ggg ctg ccg gta att aaa aag acc aaa acg ggc tac tctacc gat 864 Leu Gly Leu Pro Val Ile Lys Lys Thr Lys Thr Gly Tyr Ser ThrAsp 275 280 285 gcg gag gtt ttg gaa gag ctc ttg cct ttc cac gaa att atcggc aaa 912 Ala Glu Val Leu Glu Glu Leu Leu Pro Phe His Glu Ile Ile GlyLys 290 295 300 ata ttg aat tac cgg cag ctt atg aag tta aaa tcc act tatact gac 960 Ile Leu Asn Tyr Arg Gln Leu Met Lys Leu Lys Ser Thr Tyr ThrAsp 305 310 315 320 ggc tta atg cct tta ata aat gag cgt acc ggt aaa cttcac act act 1008 Gly Leu Met Pro Leu Ile Asn Glu Arg Thr Gly Lys Leu HisThr Thr 325 330 335 ttt aac cag acc ggt act tta acc gga cgc ctg gcg tcttcg gag ccc 1056 Phe Asn Gln Thr Gly Thr Leu Thr Gly Arg Leu Ala Ser SerGlu Pro 340 345 350 aat ctc caa aat att ccc atc cgg ttg gaa ctc ggt cggaaa tta cgc 1104 Asn Leu Gln Asn Ile Pro Ile Arg Leu Glu Leu Gly Arg LysLeu Arg 355 360 365 aag atg ttt ata cct tca ccg ggg tat gat tat att gtttcg gcg gat 1152 Lys Met Phe Ile Pro Ser Pro Gly Tyr Asp Tyr Ile Val SerAla Asp 370 375 380 tat tcc cag att gaa tta agg ctt ctt gcc cat ttt tccgaa gag ccc 1200 Tyr Ser Gln Ile Glu Leu Arg Leu Leu Ala His Phe Ser GluGlu Pro 385 390 395 400 aag ctt att gaa gct tac caa aaa ggg gag gat attcac cgg aaa acg 1248 Lys Leu Ile Glu Ala Tyr Gln Lys Gly Glu Asp Ile HisArg Lys Thr 405 410 415 gcc tcc gag gtg ttc ggt gta tct ttg gaa gaa gttact ccc gag atg 1296 Ala Ser Glu Val Phe Gly Val Ser Leu Glu Glu Val ThrPro Glu Met 420 425 430 cgc gct cat gcc aag tcg gtg aac ttc ggc att gtttat ggc att agt 1344 Arg Ala His Ala Lys Ser Val Asn Phe Gly Ile Val TyrGly Ile Ser 435 440 445 gat ttt ggt tta ggc aga gac tta aag att ccc cgggag gtt gcc ggt 1392 Asp Phe Gly Leu Gly Arg Asp Leu Lys Ile Pro Arg GluVal Ala Gly 450 455 460 aag tac att aaa aat tat ttt gcc aac tat ccc aaagtg cgg gag tat 1440 Lys Tyr Ile Lys Asn Tyr Phe Ala Asn Tyr Pro Lys ValArg Glu Tyr 465 470 475 480 ctc gat gaa ctt gtc cgt acg gca aga gaa aaggga tat gtg acc act 1488 Leu Asp Glu Leu Val Arg Thr Ala Arg Glu Lys GlyTyr Val Thr Thr 485 490 495 tta ttt ggg cga aga cgc tat att cct gag ctatct tca aaa aac cgc 1536 Leu Phe Gly Arg Arg Arg Tyr Ile Pro Glu Leu SerSer Lys Asn Arg 500 505 510 acg gtt cag ggt ttt ggc gaa agg acg gcc atgaat act ccc ctt cag 1584 Thr Val Gln Gly Phe Gly Glu Arg Thr Ala Met AsnThr Pro Leu Gln 515 520 525 ggc tcg gct gcc gat att att aag ctt gca atgatt aat gta gaa aaa 1632 Gly Ser Ala Ala Asp Ile Ile Lys Leu Ala Met IleAsn Val Glu Lys 530 535 540 gaa ctt aaa gcc cgt aag ctt aag tcc cgg ctcctt ctt tcg gtg cac 1680 Glu Leu Lys Ala Arg Lys Leu Lys Ser Arg Leu LeuLeu Ser Val His 545 550 555 560 gat gag tta gtt tta gaa gtg ccg gcg gaagag ctg gaa gag gta aaa 1728 Asp Glu Leu Val Leu Glu Val Pro Ala Glu GluLeu Glu Glu Val Lys 565 570 575 gcg ctg gta aaa ggg gtt atg gag tcg gtggtt gaa ctg aaa gtg cct 1776 Ala Leu Val Lys Gly Val Met Glu Ser Val ValGlu Leu Lys Val Pro 580 585 590 tta atc gct gaa gtt ggt gca ggc aaa aactgg tat gaa gcg aag taa 1824 Leu Ile Ala Glu Val Gly Ala Gly Lys Asn TrpTyr Glu Ala Lys 595 600 605 11 607 PRT Carboxydothermus hydrogenoformans11 Met Glu Lys Leu Ala Glu His Glu Asn Leu Ala Lys Ile Ser Lys Gln 1 510 15 Leu Ala Thr Ile Leu Arg Glu Ile Pro Leu Glu Ile Ser Leu Glu Asp 2025 30 Leu Lys Val Lys Glu Pro Asn Tyr Glu Glu Val Ala Lys Leu Phe Leu 3540 45 His Leu Glu Phe Lys Ser Phe Leu Lys Glu Ile Glu Pro Lys Ile Lys 5055 60 Lys Glu Tyr Gln Glu Gly Lys Asp Leu Val Gln Val Glu Thr Val Glu 6570 75 80 Thr Glu Gly Gln Ile Ala Val Val Phe Ser Asp Gly Phe Tyr Val Asp85 90 95 Asp Gly Glu Lys Thr Lys Phe Tyr Ser Leu Asp Arg Leu Asn Glu Ile100 105 110 Glu Glu Ile Phe Arg Asn Lys Lys Ile Ile Thr Asp Asp Ala LysGly 115 120 125 Ile Tyr His Val Cys Leu Glu Lys Gly Leu Thr Phe Pro GluVal Cys 130 135 140 Phe Asp Ala Arg Ile Ala Ala Tyr Val Leu Asn Pro AlaAsp Gln Asn 145 150 155 160 Pro Gly Leu Lys Gly Leu Tyr Leu Lys Tyr AspLeu Pro Val Tyr Glu 165 170 175 Asp Val Ser Leu Asn Ile Arg Gly Leu PheTyr Leu Lys Lys Glu Met 180 185 190 Met Arg Lys Ile Phe Glu Gln Glu GlnGlu Arg Leu Phe Tyr Glu Ile 195 200 205 Glu Leu Pro Leu Thr Pro Val LeuAla Gln Met Glu His Thr Gly Ile 210 215 220 Gln Val Asp Arg Glu Ala LeuLys Glu Met Ser Leu Glu Leu Gly Glu 225 230 235 240 Gln Ile Glu Glu LeuIle Arg Glu Ile Tyr Val Leu Ala Gly Glu Glu 245 250 255 Phe Asn Leu AsnSer Pro Arg Gln Leu Gly Val Ile Leu Phe Glu Lys 260 265 270 Leu Gly LeuPro Val Ile Lys Lys Thr Lys Thr Gly Tyr Ser Thr Asp 275 280 285 Ala GluVal Leu Glu Glu Leu Leu Pro Phe His Glu Ile Ile Gly Lys 290 295 300 IleLeu Asn Tyr Arg Gln Leu Met Lys Leu Lys Ser Thr Tyr Thr Asp 305 310 315320 Gly Leu Met Pro Leu Ile Asn Glu Arg Thr Gly Lys Leu His Thr Thr 325330 335 Phe Asn Gln Thr Gly Thr Leu Thr Gly Arg Leu Ala Ser Ser Glu Pro340 345 350 Asn Leu Gln Asn Ile Pro Ile Arg Leu Glu Leu Gly Arg Lys LeuArg 355 360 365 Lys Met Phe Ile Pro Ser Pro Gly Tyr Asp Tyr Ile Val SerAla Asp 370 375 380 Tyr Ser Gln Ile Glu Leu Arg Leu Leu Ala His Phe SerGlu Glu Pro 385 390 395 400 Lys Leu Ile Glu Ala Tyr Gln Lys Gly Glu AspIle His Arg Lys Thr 405 410 415 Ala Ser Glu Val Phe Gly Val Ser Leu GluGlu Val Thr Pro Glu Met 420 425 430 Arg Ala His Ala Lys Ser Val Asn PheGly Ile Val Tyr Gly Ile Ser 435 440 445 Asp Phe Gly Leu Gly Arg Asp LeuLys Ile Pro Arg Glu Val Ala Gly 450 455 460 Lys Tyr Ile Lys Asn Tyr PheAla Asn Tyr Pro Lys Val Arg Glu Tyr 465 470 475 480 Leu Asp Glu Leu ValArg Thr Ala Arg Glu Lys Gly Tyr Val Thr Thr 485 490 495 Leu Phe Gly ArgArg Arg Tyr Ile Pro Glu Leu Ser Ser Lys Asn Arg 500 505 510 Thr Val GlnGly Phe Gly Glu Arg Thr Ala Met Asn Thr Pro Leu Gln 515 520 525 Gly SerAla Ala Asp Ile Ile Lys Leu Ala Met Ile Asn Val Glu Lys 530 535 540 GluLeu Lys Ala Arg Lys Leu Lys Ser Arg Leu Leu Leu Ser Val His 545 550 555560 Asp Glu Leu Val Leu Glu Val Pro Ala Glu Glu Leu Glu Glu Val Lys 565570 575 Ala Leu Val Lys Gly Val Met Glu Ser Val Val Glu Leu Lys Val Pro580 585 590 Leu Ile Ala Glu Val Gly Ala Gly Lys Asn Trp Tyr Glu Ala Lys595 600 605 12 26 DNA Artificial Sequence Description of artificialsequence amplification primer 12 agcttgctgt attcccctcc atcgtg 26

We claim:
 1. A purified modified DNA polymerase that is a modified form of a DNA polymerase obtainable from Carboxydothermus hydrogenoformans, wherein said modified DNA polymerase (a) exhibits reverse transcriptase activity in the presence of magnesium ions and/or manganese ions; (b) has reduced or no 5′-3′ exonuclease activity; and (c) has substantially no RNaseH activity.
 2. A modified DNA polymerase of claim 1 that exhibits reverse transcriptase activity in the substantial absence of manganese ions.
 3. A modified DNA polymerase of claim 2 having a molecular weight of about 64 to 71 kDa as determined by SDS polyacrylamide electrophoresis.
 4. A modified DNA polymerase of claim 3 having amino acid sequence SEQ ID NO:
 11. 5. A DNA sequence encoding a modified DNA polymerase that is a modified form of a DNA polymerase obtainable from Carboxydothermus hydrogenoformans, wherein said modified DNA polymerase (a) exhibits reverse transcriptase activity in the presence of magnesium ions and/or manganese ions; (b) has reduced or no 5′-3′ exonuclease activity; and (c) has substantially no RNaseH activity.
 6. A DNA sequence of claim 5, wherein said modified DNA polymerase exhibits reverse transcriptase activity in the substantial absence of manganese ions.
 7. A DNA sequence of claim 6, wherein said modified DNA polymerase has a molecular weight of about 64 to 71 kDa as determined by SDS polyacrylamide electrophoresis.
 8. A DNA sequence of claim 7 encoding amino acid sequence SEQ ID NO:
 11. 9. A DNA sequence of claim 8 having nucleotide sequence SEQ ID NO:
 10. 10. A vector containing a DNA sequence of claim
 5. 11. A vector containing a DNA sequence of claim
 6. 12. A vector containing a DNA sequence of claim
 7. 13. A vector containing a DNA sequence of claim
 8. 14. A vector containing a DNA sequence of claim
 9. 15. A vector of claim 14 that is pΔ₂₋₂₂₅AR₄.
 16. A host cell transformed with the vector of claim
 15. 17. A host cell of claim 16 that is E.coli GA1.
 18. A process for reverse transcribing RNA, comprising carrying out a reverse transcription reaction in a magnesium buffer using a modified form of a DNA polymerase obtainable from Carboxydothermus hydrogenoformans, wherein said modified DNA polymerase (a) exhibits reverse transcriptase activity in the presence of magnesium ions and/or manganese ions; (b) has reduced or no 5′-3′ exonuclease activity; and (c) has substantially no RNaseH activity.
 19. A process of amplifying RNA, comprising carrying out a reverse transcription/polymerase chain reaction in a magnesium buffer using a combination of a first thermostable DNA polymerase and a second DNA polymerase, wherein said second DNA polymerase is a modified form of a DNA polymerase obtainable from Carboxydothermus hydrogenoformans, wherein said modified DNA polymerase (a) exhibits reverse transcriptase activity in the presence of magnesium ions and/or manganese ions; (b) has reduced or no 5′-3′ exonuclease activity; and (c) has substantially no RNaseH activity.
 20. A kit comprising an modified DNA polymerase of claim
 1. 21. A kit comprising an modified DNA polymerase of claim
 2. 22. A kit comprising an modified DNA polymerase of claim
 3. 23. A kit comprising an modified DNA polymerase of claim
 4. 